Aphthous ulcers are typically found inside the mouth, not on the genitals, though they can appear on the genitals in conditions like Behcet's disease.
The ulcer of chancroid is a painful, soft ulcer with a purulent base that is not preceded by a vesicular stage, unlike herpes.
Genital ulcers from EBV are rare and would be diagnosed by exclusion and specific viral testing in the absence of evidence for HSV.
The primary lesion of LGV is a small, painless, transient papule or ulcer that often goes unnoticed, followed by dramatic, painful inguinal lymphadenopathy (buboes).
The classic primary chancre of syphilis is a single, painless ulcer with a clean base and a firm, indurated border, which is morphologically and symptomatically distinct from the multiple, painful, vesicular-then-ulcerative lesions of herpes.